6-79399535-A-G

Variant names:

• chr6-79399535-A-G
• rs17799762

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0857 in 152,226 control chromosomes in the GnomAD database, including 608 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.086 (608 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0200
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.118 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0858 AC: 13055 AN: 152108 Hom.: 608 Cov.: 32

Gnomad AFR AF: 0.0470

Gnomad AMI AF: 0.0175

Gnomad AMR AF: 0.0906

Gnomad ASJ AF: 0.164

Gnomad EAS AF: 0.101

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0519

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.106

Gnomad OTH AF: 0.108

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0857 AC: 13052 AN: 152226 Hom.: 608 Cov.: 32 AF XY: 0.0838 AC XY: 6238 AN XY: 74430

African (AFR) AF: 0.0469 AC: 1949 AN: 41546

American (AMR) AF: 0.0905 AC: 1383 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.164 AC: 568 AN: 3466

East Asian (EAS) AF: 0.101 AC: 520 AN: 5160

South Asian (SAS) AF: 0.127 AC: 611 AN: 4818

European-Finnish (FIN) AF: 0.0519 AC: 552 AN: 10626

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.106 AC: 7197 AN: 68010

Other (OTH) AF: 0.108 AC: 228 AN: 2106

Alfa AF: 0.0981 Hom.: 215

Bravo AF: 0.0863

Asia WGS AF: 0.108 AC: 378 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.9
DANN	Benign	0.73
PhyloP100		-0.020

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs17799762; hg19: chr6-80109252;